Layout genomes

Layout genomes

Usage

layout_genomes(
  seqs = NULL,
  genes = NULL,
  feats = NULL,
  links = NULL,
  infer_bin_id = seq_id,
  infer_start = min(start, end),
  infer_end = max(start, end),
  infer_length = max(start, end),
  adjacent_only = TRUE,
  ...
)

Arguments

seqs

A data.frame or a character vector with paths to files containing sequence data. Data columns:

• required: seq_id,length

• recognized: bin_id,start,end,strand

genes, feats

A data.frame, a list of data.frames, or a character vector with paths to files containing gene data. Each item is added as feature track.

For a single data.frame the track_id will be "genes" and "feats", respectively. For a list, track_ids are parsed from the list names, or if names are missing from the name of the variable containing each data.frame. Data columns:

• required: seq_id,start,end

• recognized: strand,bin_id,feat_id,introns

links

A data.frame or a character vector with paths to files containing link data. Each item is added as links track. Data columns:

• required: seq_id,seq_id2

• recognized: start,end,bin_id,start2,end2,bin_id2,strand

infer_length, infer_start, infer_end, infer_bin_id

used to infer pseudo seqs if only feats or links are provided, or if no bin_id column was provided. The expressions are evaluated in the context of the first feat or link track.

By default subregions of sequences from the first to the last feat/link are generated. Set infer_start to 0 to show all sequences from their true beginning.

adjacent_only

Indicates whether links should be created between adjacent sequences/chromosomes only. By default it is set to adjacent_only = TRUE. If FALSE, links will be created between all sequences

(not recommended for large data sets)

...

additional parameters, passed to layout

Value

gggenomes_layout object